DMITRY I. OSOLODKIN

Personal Information

• E-mail: dmitry_o@qsar.chem.msu.ru

Education

• Ph. D. thesis: «Molecular Design of GSK-3 Inhibitors» (summary).

• Ph. D. in Chemistry studies, Department of Chemistry, Moscow State University: 2006 to 2011 (scientific advisor Dr. Vladimir A. Palyulin)

• Master of Science in Medicinal Chemistry, Department of Chemistry, Moscow State University: 2001 to 2006 (scientific advisor Dr. Vladimir A. Palyulin)

Current Status

• Research associate, Group of Molecular Modelling and QSAR, Department of Chemistry, Moscow State University.

Scientific interests

• Chemoinformatics

• Kinase inhibitors

• Medicinal chemistry

• Molecular modelling

• Structure based drug design

• Virtual screening

Research Topics

• Design of the kinase inhibitors;

• Modelling and structural classification of bacterial eukaryotic type serine/threonine protein kinases (collaboration with The Institute of General Genetics RAS);

• Modelling of the dynamics of E glycoproteins of tick-borne encephalitis virus, design of new lead molecules interacting with these proteins (collaboration with The Institute of Poliomyelitis and Viral Encephalitides RAMS).

• Modelling of the CHASE domain structure and functioning for cytokinin receptors (collaboration with The Institute of Plant Physiology RAS)

Languages

• Russian — native

• English — fluent speech and scientific writing

• Latin — basic knowledge.

• Participated in the translation of the book «Molecular Modelling. Basic Principles and Applications» by H.-D. Höltje, W. Sippl, G. Folkers, D. Rognan into Russian.

Papers

• Kozlovskaya L.I., Osolodkin D.I., Karganova G.G. Analysis of molecular dynamics of TBEV variants' E proteins based on difference of correlation matrices. Medical Virology. 2013, XXVII (2), 42-53.

• Osolodkin D.I., Kozlovskaya L.I., Dueva E.V., Dotsenko V.V., Rogova Y.V., Frolov K.A., Krivokolysko S.G., Romanova E.G., Morozov A.S., Karganova G.G., Palyulin V.A., Pentkovski V.M., Zefirov N.S. Inhibitors of Tick-Borne Flavivirus Reproduction from Structure-Based Virtual Screening. ACS Medicinal Chemistry Letters. 2013, 4, 869–874. doi: 10.1021/ml400226s.

• Oliferenko P.V., Oliferenko A.A., Poda G.I., Osolodkin D.I., Pillai G.G., Bernier U.R., Tsikolia M., Agramonte N.M., Clark G.G., Linthicum K.J., Katritzky A.R. Promising Aedes aegypti repellent chemotypes identified through integrated QSAR, virtual screening, synthesis, and bioassay. PLoS One. 2013, 8, e64547. doi: 10.1371/journal.pone.0064547. PMC3765160. PMID: 24039693.

• Steklov M.Y., Lomin S.N., Osolodkin D.I., Romanov G.A. Structural basis for cytokinin receptor signaling: An evolutionary approach. Plant Cell Reports. 2013, 32, 781-793. doi: 10.1007/s00299-013-1408-3. PMID: 23525743.

• Osolodkin D.I., Palyulin V.A., Zefirov N.S. Glycogen synthase kinase 3 as an anticancer drug target: Novel experimental findings and trends in the design of inhibitors. Current Pharmaceutical Design. 2013, 19, 665-679. doi: 10.2174/138161213804581972. PMID: 23016861.

• Lomin S.N., Krivosheev D.M., Steklov M.Y., Osolodkin D.I., Romanov G.A. Receptor properties and features of cytokinin signaling. Acta Naturae. 2012, 4 (3), 31-45. PMC3491891. PMID: 23150802.

• Osolodkin D.I., Kozlovskaya L.I., Palyulin V.A., Pentkovski V.M., Karganova G.G., Zefirov N.S. A molecular model and Monte Carlo simulation of flavivirus envelope building block. Biochemical and Biophysical Research Communications. 2012, 425, 207-211. doi: 10.1016/j.bbrc.2012.07.069. PMID: 22835932.

• Zakharevich N.V., Osolodkin D.I., Artamonova I.I., Palyulin V.A., Zefirov N.S., Danilenko V.N. Signatures of the ATP binding pocket as a basis for structural classification of the serine/threonine protein kinases of gram-positive bacteria. Proteins: Structure, Function, and Bioinformatics. 2012, 80, 1363-1376. doi: 10.1002/prot.24032. PMID: 22275035.

• Milaeva E.R., Meleshonkova N.N., Shpakovsky D.B., Paulavets V.V., Orlova S.I., Osolodkin D.I., Palyulin V.A., Loginov S.V., Storozhenko P.A., Zefirov N.S. Polytopic zinc dipicolylamine complex containing a ferrocene moiety as a new lipoxygenase LOX I-B inhibitor. Doklady Chemistry. 2012, 443, 77-79. doi: 10.1134/S0012500812030032.

• Shulga D.A., Osolodkin D.I., Palyulin V.A., Zefirov N.S. Simulation of Intramolecular Hydrogen Bond Dynamics in Manzamine A as a Sensitive Test for Charge Distribution Quality. Natural Product Communications. 2012, 7, 295-299. PMID: 22545399.

• Milaeva E.R., Orlova S.I., Osolodkin D.I., Palyulin V.A., Fursova E.Y., Ovcharenko V.I., Zefirov N. S. Copper complexes with nitronylnitroxyl radicals as lipoxygenase inhibitors with antioxidant activity. Russian Chemical Bulletin. 2011, 60, 2564-2571. doi: 10.1007/s11172-011-0394-2.

• Karpov P.V., Osolodkin D.I., Baskin I.I., Palyulin V.A., Zefirov N.S. One-class classification as a novel method of ligand-based virtual screening: the case of glycogen synthase kinase 3β inhibitors. Bioorganic & Medicinal Chemistry Letters, 2011, 21, 6728-6731. doi: 10.1016/j.bmcl.2011.09.051. PMID: 21983440.

• Osolodkin D.I., Palyulin V.A., Zefirov N.S. Structure-based virtual screening of glycogen synthase kinase 3β inhibitors: Analysis of scoring functions applied to large true actives and decoy sets. Chemical Biology & Drug Design. 2011, 78, 378-390. doi: 10.1111/j.1747-0285.2011.01159.x. PMID: 21679374. The Dataset.

• Palyulin V.A., Osolodkin D.I., Zefirov N.S. Virtual screening workflow for glycogen synthase kinase 3β inhibitors: convergence of ligand-based and structure-based approaches. Journal of Cheminformatics. 2011, 3 (Suppl. 1), P17. doi: 10.1186/1758-2946-3-S1-P17.

• Osolodkin D.I., Zakharevich N.V., Palyulin V.A., Danilenko V.N., Zefirov N.S. Bioinformatic Analysis of Glycogen Synthase Kinase 3: Human versus Parasite Kinases. Parasitology. 2011, 138, 725-735. doi: 10.1017/S0031182011000151. PMID: 21349219.

• Danilenko V.N., Osolodkin D.I., Lakatosh S.A., Preobrazhenskaya M.N., Shtil A.A. Bacterial Eukaryotic Type Serine-Threonine Protein Kinases: From Structural Biology to Targeted Anti-Infective Drug Design. Current Topics in Medicinal Chemistry. 2011, 11, 1352-1369. doi: 10.2174/156802611795589566. PMID: 21513496.

• Tsareva D.A., Osolodkin D.I., Shulga D.A., Oliferenko A.A., Pisarev S.A., Palyulin V.A., Zefirov N.S. General Purpose Electronegativity Relaxation Charge Models Applied to CoMFA and CoMSIA Study of GSK-3 Inhibitors. Molecular Informatics. 2011, 30, 169-180. doi: 10.1002/minf.201000141.

• Osolodkin D.I., Shulga D.A., Palyulin V.A., Zefirov N.S. Interaction of Manzamine A with Glycogen Synthase Kinase 3β: A Molecular Dynamics Study. Russian Chemical Bulletin. 2010, 59, 1983-1993. doi: 10.1007/s11172-010-0344-4. Russian version.

• Bekker O.B., Alekseeva M.G., Osolodkin D.I., Palyulin V.A., Elizarov S.M., Zefirov N.S., Danilenko V.N. New Test System for Serine/Threonine Protein Kinase Inhibitors Screening: E. coli APHVIII/Pk25 design. Acta Naturae. 2010, 2 (3), 110-121. PMID: 22649658.

• Palyulin V.A., Radchenko E.V., Osolodkin D.I., Chupakhin V.I., Zefirov N.S. Ionotropic GABA Receptors: Modelling and Design of Selective Ligands. Journal of Cheminformatics. 2010, 2 (Suppl. 1), P49. doi: 10.1186/1758-2946-2-S1-P49.

• Palyulin V.A., Osolodkin D.I., Zefirov N.S. Virtual Screening Workflow for Glycogen Synthase Kinase 3β Inhibitors. Drugs of the Future. 2010, 35 (Suppl. A), 176. Full text.

• Osolodkin D.I., Shulga D.A., Tsareva D.A., Oliferenko A.A., Palyulin V.A., Zefirov N.S. The Choice of Atomic Charges Calculation Scheme in 3D-QSAR Modelling of GSK-3β Inhibition by Paullones. Doklady Biochemistry Biophysics. 2010, 434, 274-278. doi: 10.1134/S1607672910050145. PMID: 20960255. Russian version. Elibrary.

• Kozlovskaya L.I., Osolodkin D.I., Shevtsova A.S., Romanova L.I., Rogova Y.V., Dzhivanian T.I., Lyapustin V.N., Pivanova G.P., Gmyl A.P., Palyulin V.A., Karganova G.G. GAG-binding variants of tick-borne encephalitis virus. Virology. 2010, 398, 262-272. doi: 10.1016/j.virol.2009.12.012. PMID: 20064650.

• Osolodkin D.I., Chupakhin V.I., Palyulin V.A., Zefirov N.S. Molecular modeling of ligand-receptor interactions in GABA_C receptor. Journal of Molecular Graphics and Modelling. 2009, 27, 813-821. doi: 10.1016/j.jmgm.2008.12.004. PMID: 19167917.

• Osolodkin D.I., Chupakhin V.I., Palyulin V.A., Zefirov N.S. Modeling and analysis of ligand-receptor interactions in the GABAc receptor. Doklady Biochemistry Biophysics. 2007, 412, 25-28. doi: 10.1134/S1607672907010085. PMID: 17506348. Russian version. Elibrary.